Modified yeast consuming L-arabinose

ABSTRACT

The present invention relates to a method for producing a L-arabinose utilizing yeast strain for the production of ethanol, whereby a yeast strain is modified by introducing and expressing araA gene (L-arabinose isomerase), araB gene (L-ribulokinase D 121 -N) and araD gene (L-ribulose-5-P 4-epimerase) and carrying additional mutations in its genome or overexpressing a TAL1 (transaldolase) gene, enabling it to consume L-arabinose, to use it as the only carbon source, and to produce ethanol, as well as a method for producing ethanol using such a modified strain.

TECHNICAL FIELD

The present invention relates to a modified yeast strain, preferably a Saccharomyces cerevisiae, consuming L-arabinose while producing ethanol, as well as a method for producing ethanol.

BACKGROUND OF THE INVENTION

Fuel ethanol is considered as a suitable alternative to fossil fuels and it can be produced from plant biomass, which is a low cost and renewable resource available in large amounts. For this reason cellulose biomass, which includes agricultural residues, paper wastes, wood chips, etc., is an ideal abundantly available source of sugars for the fermentation to ethanol. For example when glucose is produced from cereals, hemi-cellulose-containing by-products mainly consisting of the pentose sugars arabinose and xylose (arabinoxylan) are generated. These are presently used as a low price cattle feed. But this resource could be utilized in a more profitable way if it would be integrated into existing starch processing which yields ethanol and starch derivatives.

In the context of conversion of hemi-cellulose sugars, fermentability of L-arabinose becomes important. The approximation is often made that hydrolysates generated by dilute acid pretreatment, contain only D-xylose because this is the most abundant hemi-cellulose sugar. Resulting from this most studies on conversion of hemi-cellulose hydrolysates focus on the conversion of D-xylose. However hemi-cellulose as a heteropolysaccharide contains pentosans and hexosans. Although xylan is the dominant pentosan and glucomannan is the dominant hexosan the levels of arabinan are significant in some biomass materials. In particular arabinan levels are significant in herbaceous species where it represents up to 10-20% of total non-glucan carbohydrate. Microbial biocatalysts selected to develop or ferment hydrolysates derived from materials with high arabinan content must therefore exhibit the ability to ferment L-arabinose as well as xylose and preferably also other sugars to ethanol.

Many types of yeast, especially Saccharomyces cerevisiae and related species have traditionally been used for fermenting glucose based feedstocks to ethanol by anaerobic fermentation because they are the safest and most effective micro organisms for fermenting sugars to ethanol. But these superior glucose fermenting yeasts are unable to ferment xylose and L-arabinose and are also unable to use these pentose sugars for growth. A few other yeast species such as Pichia sdpitis and Candida shehatae can ferment xylose to ethanol; however, they are not as effective as Saccharomyces for fermentation of glucose and have a relatively low ethanol tolerance. Thus, they are not suitable for large scale industrial production of ethanol from biomass. Some yeast can utilize L-arabinose for growth but no yeast can ferment it to commercial amounts of ethanol. Unlike yeasts and fungi, most bacteria, including E. coli and Bacillus subtilis, can utilize L-arabinose for aerobic growth and are also able to ferment it to various products including ethanol.

Sedlak & Ho, Enzyme Microb Technol 28, (2001) pp. 16-24 discloses an expression of E. coli araBAD operon encoding enzymes for metabolizing L-arabinose in Saccharomyces cerevisiae. The strain hereby expresses araA, araB and araD, but is incapable of producing any ethanol.

SUMMARY OF THE INVENTION

It has now been possible to solve this problem, whereby a new Saccharomyces cerevisiae yeast strain able to consume L-arabinose, has been created, and to produce ethanol.

DETAILED DESCRIPTION OF THE PATENT INVENTION

It has now surprisingly been found possible to overcome the problem of having a yeast consuming L-arabinose by means of the present invention by obtaining a method for producing a L-arabinose utilizing yeast strain for the production of ethanol, which method is characterized in that a yeast strain is modified by introducing and expressing B. subtilis araA gene (L-arabinose isomerase), E. coil araB gene (L-ribulokinase) and E. coli araD gene (L-ribulose-5-P 4-epimerase), and carrying additional mutations in its genome or overexpressing the S. cerevisiae TAL1 (transaldolase) gene, enabling it to consume L-arabinose, and to produce ethanol.

The invention will be described more in detail in the following by reference to a number of experiments described explaining the nature of the invention.

The application further encompasses the Saccharomyces cerevisiae strain JBY25-4M (DSM 15560) and Saccharomyces cerevisiae strain JBY24-3T (DSM 15559) which were deposited at Deutsche Sammiung von Mikroorganismen und Zelikulturen on Apr. 4, 2003 under the Budapest Convention.

First, the E. coli genes araA (L-arabinose isomerase), araB (L-ribulokinase) and araD (L-ribulose-5-P 4-epimerase) have been cloned and overexpressed behind the strong HXT7 promoter fragment on multicopy vectors in S. cerevisiae CEN.PK-strains. Whereas araA did not produce any L-arabinose isomerase activity in the yeast transformants, araB overexpression produced up to 0.7 U/mg protein L-ribulokinase activity and araD produced up to 0.13 U/mg protein L-ribulose-5-P 4-epimerase activity. Transformation of CEN.PK2-1C with all three constructs together did not allow the transformants to grow on L-arabinose medium. It has been shown that the yeast galactose permease (Gal2) is able to transport L-arabinose [J. Bacteriol. 103, 671-678 (1970)]. Simultaneous overexpression of GAL2 behind the ADH1 promoter together with the bacterial L-arabinose metabolising genes did also not allow the transformants to grow on L-arabinose medium.

Second, cloning and overexpression of the Bacillus subtilis araA gene behind the strong HXT7 promoter fragment on multicopy vectors in the S. cerevisiae CEN.PK2-1C strain resulted in an active protein in-yeast, which produced L-arabinose isomerase activity in the order of at least some mU/mg protein. Similarly, overexpression of the Mycobacterium smegmatis araA gene behind the strong HXT7 promoter fragment on a multicopy vector in the S. cerevisiae CEN.PK2-1C strain produced L-arabinose isomerase activity.

Then, transformants expressing the B. subtilis araA gene together with the E. coli genes araB and araD as well as the yeast GAL2 gene were incubated in liquid media (synthetic complete or synthetic complete/0.1% yeast extract/0.2% peptone) with L-arabinose as the sole carbon source for several weeks. After 4-5 days of incubation the transformants started to grow slowly in these media, in contrast to a strain containing only four empty vectors. Whenever the cells reached an OD₆₀₀ of 3-4, they were inoculated in fresh medium at an OD₆₀₀ of 0.3, and grown further. Growth became faster after 10 days. These observations indicate the occurrence of spontaneous suppressor mutations enabling the cells to use L-arabinose more efficiently. Otherwise, the cells might become somehow adapted to the use of L-arabinose.

To distinguish between suppressor mutations or an adaptation process, the mutant transformants were grown on glucose medium and then shifted again on arabinose medium. They started to grow on arabinose medium with only a short lag-phase indicating that indeed they contain specific mutations enabling the cells to grow on arabinose. The activities of all three heterologous enzymes were measured in crude extracts of the original and the mutant transformants. Whereas the activities of L-ribulose-5-P 4-epimerase and L-arabinose isomerase were similar in both strains, the L-ribulokinase activity was strongly reduced in the mutant transformants.

When the mutant transformants were selected for loss of their plasmids they were no longer able to grow on arabinose. The plasmids were re-isolated and amplified in E. coli. The re-isolated plasmids were transformed into a CEN.PK2-1C wild-type strain. When growth on arabinose of these new transformants was compared to the original mutant transformants, the lag-phase on arabinose medium was significantly prolonged indicating that additional genomic mutations had occurred in the mutant transformants enabling them to grow efficiently on arabinose. Different combinations of original and re-isolated plasmids were transformed into the mutant JBY25 strain. It turned out that replacing the re-isolated GAL2, araD and araA plasmids by the corresponding original plasmids did only slightly affect the ability to grow on arabinose. However, replacing the re-isolated araB (L-ribulokinase) plasmid by the corresponding original plasmid resulted in strongly reduced growth on arabinose.

When the complete re-isolated L-ribulokinase gene was sequenced it showed one mutation, which leads to an exchange of amino acid 121 Asp for an Asn in the conserved sugar kinase domain of the kinase. Determination of the kinetics of the mutant enzyme revealed that its Km value for L-ribulose was increased and the Vmax was decreased.

Growth experiments with the wild-type and mutant kinases expressed from centromeric plasmids in strain JBY25 together with the re-isolated isomerase and epimerase plasmids have also been performed. In case of the mutant kinase this centromeric plasmid did not confer good growth on L-arabinose to the transformants. But the transformants carrying the wild-type kinase on a centromeric plasmid showed better growth than those transformed with the overexpressed kinase. This is another indication that the reduced activity of the kinase is important for better growth on L-arabinose.

To find out whether all four plasmids carrying the Bacillus subtilis L-arabinose isomerase, the E. coli L-ribulokinase and L-ribulose 5-P 4-epimerase and the yeast Gal2galactose permease, respectively, are necessary for growth on L-arabinose, the mutant strain was transformed with different combinations of re-isolated and empty plasmids (without any gene for L-arabinose metabolism). Transformants lacking the L-arabinose isomerase, the L-ribulokinase or the L-ribulose 5-P 4-epimerase but transformed with the other three re-isolated plasmids did not show any growth on L-arabinose indicating that these genes are absolutely necessary for the utilization of L-arabinose. Transformants lacking the overexpressed galactose permease are able to grow on L-arabinose medium, but with slightly decreased growth rates as compared to the mutant strain containing all four re-isolated plasmids, indicating that over-expression of a transporter is not necessary for growth on L-arabinose but can improve it.

To test whether only one or more mutations in the genome of the CEN.PK2-1C wild-type strain enable the transformants to grow on L-arabinose, and whether these mutation(s) are recessive or dominant, the mutant strain and also the wild-type strain, each transformed with the four plasmids for L-arabinose metabolism were crossed with a haploid wild-type strain. Afterwards, growth on L-arabinose was investigated. The diploid mutant strain exhibited faster growth on L-arabinose than the diploid control strain. But the diploid mutant strain did not grow as well as the haploid mutant strain transformed with the four plasmids. The diploid mutant strain was sporulated and tetrade analysis was performed. The results indicate that there is more than one mutation in the genome of the strain with at least one being dominant and another one being recessive.

Moreover, overexpression of S. cerevisiae TAL1 (transaldolase) together with B. subtilis araA (L-arabinose isomerase), mutant E. coli araB (L-ribulokinase), and E. coli araD (L-ribulose-5-P 4-epimerase) resulted in growth on L-arabinose already in the CEN.PK2-1C wild-type strain.

Ethanol production was determined with the IBY25 mutant strain transformed with the four re-isolated plasmids and incubated in a growth medium with 20 g/L L-arabinose. Under oxygen-limiting conditions at a culture OD_(600nm)=15-20, ethanol production rates reached up to 0.06 g ethanol/g dry weight and hour.

We have now demonstrated that it is possible to transfer the method for producing an L-arabinose utilizing yeast strain to other Saccharomyces cerevisiae strains that are different from the CEN.PK strains.

We have used the W303 S. cerevisiae strain that is not related to the CEN.PK strains, and have transformed this strain with the plasmids expressing B. subtilis araA gene (L-arabinose isomerase), the mutant E. coli araB gene with reduced activity (L-ribulokinase), E. coli araD gene (L-ribulose-5-P 4-epimerase), and S. cerevisiae TAL1 (transaldolase) gene.

The transformants could grow on a defined medium with L-arabinose as the sole carbon source, although very slowly. Then, cells were incubated in liquid medium (synthetic complete/0.1% yeast extract/0.2% peptone) with L-arabinose as the sole carbon source for several days. After 4-5 days of incubation the transformants started to grow faster in this medium, in contrast to a W303 strain containing only four empty vectors. Whenever the cells reached an OD₆₀₀ of 3-4, they were inoculated in fresh medium at an OD₆₀₀ of 0.3, and grown further. Finally, after 20 days this resulted in a strain able to grow on L-arabinose medium much more faster, and able to ferment L-arabinose to ethanol.

The invention is a modified yeast strain expressing the bacterial B. subtilis araA gene (L-arabinose isomerase), E. coli mutant araB gene (L-ribulokinase D¹²¹-N) and E. coli araD gene (L-ribulose-5-P 4-epimerase), and carrying additional mutations in its genome or overexpressing the S. cerevisiae TAL1 (transaldolase) gene, enabling it to consume L-arabinose, to use it as the only carbon source, and to produce ethanol.

Normally the growth medium will contain about 20 g of L-arabinose/L. However, growth and production of ethanol will occur between 2 and 200 g/L. There is no need for further sugars, and thus L-arabinose can be used alone. It is possible that co-consumption of xylose and arabinose could work, but this has not been determined so far. 

1. A method for producing an L-arabinose utilizing Saccharomvces cerevisiae east strain for the production of ethanol, wherein a yeast strain is modified by introducing and expressing an araA gene (L-arabinose isomerase), an araB gene (L-ribulokinase) and an araD gene (L-ribulose-5-P 4-epimerase), and carrying additional mutations in its genome or overexpressing a TAL1 (transaldolase) gene, enabling it to consume L-arabinose, and to produce ethanol thereby from a medium comprising L-arabinose, whereby the yeast strain is further modified by expressing a mutant form of the E. coli L-ribulokinase enzyme with reduced activity.
 2. The method according to claim 1, wherein the araA gene is a B. subtilis araA gene.
 3. The method according to claim 1, wherein the araA gene is a M. smegmatis araA gene.
 4. The method according to claim 1, wherein the araB gene is a E. coli araB gene.
 5. The method according to claim 1, wherein the araD gene is an E. coli araD gene.
 6. The method according to claim 1, wherein the TAL1 gene is an S. cerevisiae TAL1 gene.
 7. (canceled)
 8. The method according to claim 1, wherein the Saccharomyces cerevisiae strain is a CEN.PK strain, preferably a CEN.PK2-1C.
 9. The method according to claim 1, wherein the Saccharomyces cerevisiae strain is a Saccharomyces cerevisiae W303-strain.
 10. (canceled)
 11. The method according to claim 1, wherein the yeast strain is further modified by overexpressing the yeast GAL2 gene.
 12. The method according to claim 1, wherein the araB gene is placed behind a weak promoter.
 13. The method according to claim 1, wherein the modifications are made behind the strong HXT7 promoter fragment on multicopy vectors in S. cerevisiae CEN.PK-strains.
 14. The method according to claim 1, wherein the modifications are made behind the strong HAX7 promoter fragment on multicopy vectors in Saccharomyces cerevisiae W303-strains.
 15. The method according to claim 1, wherein the amount of L-arabinose of the growth medium is 2 to 200 g/L.
 16. The method according to claim 1, wherein the strain is Saccharomyces cerevisiae strain JBY25-4M with DSM accession number
 15560. 17. The method according to claim 1, wherein the strain is Saccharomyces cerevisiae strain JBY24-3T with a DSM accession number
 15559. 18. A method for producing ethanol by fermenting yeast, wherein a modified yeast according to claim 1 ferments a growth medium containing L-arabinose.
 19. The method according to claim 18, wherein the amount of L-arabinose of the growth medium is 2 to 200 g/L. 